Well,
You have already cut up the deck pretty good with the chainsaw...Nightfighter said it first...... I would have started by buying some GIT-ROT and drill a bunch of 1/4" holes in the top of the deck. This thin epoxy is water thin and soaks into rotton wood and really is the balls. It is made just for this kind of situation. Kind of late for that.
How old is the boat? I wouldn't hesitate to put plywood back in, some Okeomo good stuff. I think any wood put into that situation (encapsulated) over time will rot since all the wholes are in it for the stanchions. Glue it in fill it glass it etc.
If going with oak, don't use red, go white. Some of the best wood boats are framed and planked in white oak, not always easy to find.
Not sure the best easiest way for the fasteners since you have no access. Your plate idea is interesting. Many railings like this are not thru bolted but just screwed and yes over time they get loose so bolting would be best for the long haul.
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